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freebsd-ports/biology
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Danilo G. Baio 75a5f7f076 Update Sphinx 
- Repocopy textproc/py-sphinx to textproc/py-sphinx18

  Update it to 1.8.5 (latest version from 1.8.X).
  This version supports Python 2 and 3.
  Add test target.

- textproc/py-sphinx: Update to 3.0.2

  Python 3 only (3.5+).
  Add test target.

- Mk/Uses/python.mk: Add PY_SPHINX

  Shared macro to use with flavors and not break
  ports with USES=python (all versions).

  Python >=3.5  --> textproc/py-sphinx (v3.0.2)
  Python < 3.5  --> textproc/py-sphinx18 (v1.8.5)

  All ports that uses sphinx were changed to use the new variable
  ${PY_SPHINX} in the dependency line, exceptions:

    * Ports that fails to build with sphinx 3.0.2 because of code.
      They are pointing to textproc/py-sphinx18 directly.
      There aren't many ports.

    * Ports that doesn't know Python flavors.

- Add several patches to fix Sphinx consumers

  The most common issues are related with pkg-plist, the output
  files from Sphinx changes between versions, keep this dynamically
  is the better approach.

  This will save time in future sphinx updates.

PR:		245629
Exp-run by:	antoine
2020-05-11 23:51:58 +00:00
..
abyss Drop dependency on devel/openmp 2020-03-08 21:56:36 +00:00
artemis Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
avida biology/avida: unbreak on powerpc64 2019-10-23 16:25:10 +00:00
babel
bamtools devel/jsoncpp: Update 1.8.1 -> 1.9.2 2020-01-13 21:38:35 +00:00
bcftools math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
bedtools biology/bedtools: Upgrade to 2.29.2 2019-12-19 01:04:11 +00:00
biococoa Return theraven's ports to the pool after safekeeping his commit bit. 2020-03-05 20:49:05 +00:00
bolt-lmm Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas. 2020-05-06 16:11:14 +00:00
bowtie
bowtie2 Update devel/tbb to 2020.2 and bump dependent port's revisions 2020-04-01 14:14:51 +00:00
bwa
canu biology/canu: Upgrade to 2.0 2020-03-20 18:14:23 +00:00
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks biology/cufflinks: Update 2.2.1-83 -> 2.2.1-89 2020-03-31 06:42:22 +00:00
cytoscape Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
ddocent
diamond biology/diamond: Update to version 0.9.32 2020-04-24 23:04:14 +00:00
dsr-pdb devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
emboss - update libgd to 2.3.0 2020-05-04 21:31:39 +00:00
exonerate
fasta
fasta3
fastahack biology/fastahack: Upgrade to 1.0.0 2019-10-06 21:34:32 +00:00
fastdnaml
fastool
fastp biology/fastp: Upgrade to 0.20.1 2020-04-09 16:17:02 +00:00
fastqc biology/fastqc: Upgrade to 0.11.8 2019-09-21 02:44:54 +00:00
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
gatk Preserve Gradle 6.2.2 for biology/gatk 2020-05-06 13:11:49 +00:00
gcta Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas. 2020-05-06 16:11:14 +00:00
gemma Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
gff2ps
gmap
gperiodic - Update WWW 2020-01-19 09:30:22 +00:00
graphlan Deprecate a few ports 2020-02-23 15:25:53 +00:00
grappa
groopm Deprecate a few ports 2020-02-23 15:25:53 +00:00
haplohseq Deprecate some ports using deprecated version of python 2020-03-08 17:01:46 +00:00
hhsuite biology/hhsuite: fix build on powerpc64 elfv2 2020-05-11 19:33:32 +00:00
hisat2
hmmer biology/hmmer: update to 3.3 2020-01-29 05:55:12 +00:00
htslib
hyphy biology/hyphy: Update to version 2.5.12 2020-05-03 02:08:19 +00:00
igv Deprecate java/openjfx8-devel consumers 2020-03-19 09:33:13 +00:00
infernal biology/infernal: update to 1.1.3 2020-01-27 17:57:14 +00:00
iolib
iqtree biology/iqtree: Update to version 2.0.4 2020-05-02 20:32:33 +00:00
jalview Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
jellyfish biology/jellyfish: Patch for clang 10 2020-03-07 19:25:54 +00:00
kallisto kallisto: Patch for build with GCC 2020-04-01 23:35:38 +00:00
lagan
lamarc
libbigwig
libgtextutils
libsbml Clean up Makefile 2020-02-08 19:01:40 +00:00
linux-foldingathome Update to 7.6.13 2020-05-09 13:21:29 +00:00
mafft
mapm3
migrate
minimap2
molden Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
mopac
mothur Update devel/gmake to 4.3. 2020-05-09 19:24:49 +00:00
mrbayes - Swap back from net/openmpi3 to net/openmpi 2020-04-21 21:47:57 +00:00
mummer
muscle biology/muscle: unbreak in -CURRENT 2020-01-17 16:49:03 +00:00
ncbi-blast+ biology/ncbi-blast+: Upgrade to 2.10.0 2019-12-26 16:21:17 +00:00
ncbi-cxx-toolkit Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
ncbi-toolkit biologi/ncbi-toolkit: Remove dependency on libXp 2019-09-28 10:52:57 +00:00
ngs-sdk biology/ngs-sdk: Update 2.10.4 -> 2.10.5 2020-04-04 20:09:00 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene Update *_DEPENDS 2020-01-08 18:36:30 +00:00
p5-Bio-Cluster Update *_DEPENDS 2019-12-08 16:57:18 +00:00
p5-Bio-Coordinate Cosmetic change 2020-04-02 12:01:30 +00:00
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL Add p5-Bio-DB-EMBL 1.7.4 2019-12-08 16:49:19 +00:00
p5-Bio-DB-NCBIHelper Add p5-Bio-DB-NCBIHelper 1.7.6 2019-12-08 16:49:25 +00:00
p5-Bio-FeatureIO Cosmetic change 2020-04-02 12:01:35 +00:00
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-Bio-Variation Update to 1.7.5 2020-01-08 18:36:35 +00:00
p5-BioPerl Update to 1.007007 (1.7.7) 2019-12-08 16:57:23 +00:00
p5-BioPerl-Run Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago 2020-01-08 18:36:40 +00:00
p5-transdecoder
p5-TrimGalore biology/p5-TrimGalore: Upgrade to 0.6.5 2019-11-26 16:20:12 +00:00
paml biology/paml: Update to version 4.9j 2019-11-22 15:32:40 +00:00
pbbam devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
pbcopper Mark BROKEN: fails to build 2020-03-10 14:17:19 +00:00
pbseqan biology/unanimity and dependencies: Flag as no longer open source 2019-11-24 15:53:00 +00:00
pear-merger
phrap
phred
phylip Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
phyml - Swap back from net/openmpi3 to net/openmpi 2020-04-21 21:51:56 +00:00
plink Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas 2020-05-06 16:39:12 +00:00
primer3
prodigal biology/prodigal: Eliminate a very old version from the portscout discovery process 2019-10-12 15:40:21 +00:00
prodigy-lig
protomol Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
psi88
py-biom-format Deprecate a few ports 2020-02-23 15:25:53 +00:00
py-biopython
py-bx-python biology/py-bx-python: Update 0.8.6 -> 0.8.8 2020-02-15 20:08:30 +00:00
py-cutadapt biology/py-cutadapt: Upgrade to 2.7 2019-11-23 14:45:53 +00:00
py-dnaio biology/py-dnaio: Upgrade to 0.4.1 2019-11-23 14:40:00 +00:00
py-fastTSNE Drop dependency on devel/openmp 2020-03-08 21:56:36 +00:00
py-Genesis-PyAPI
py-gffutils biology/py-gffutils: Update 0.9 -> 0.10 2019-12-31 05:16:09 +00:00
py-gtfparse
py-loompy
py-macs2 biology/py-macs2: Upgrade to 2.2.7.1 2020-04-14 12:13:55 +00:00
py-multiqc biology/py-multiqc: Upgrade to 1.8 2019-11-26 16:25:08 +00:00
py-orange3-bioinformatics
py-orange3-single-cell Update Sphinx 2020-05-11 23:51:58 +00:00
py-pyfaidx
py-pysam biology/py-pysam: Update 0.15.3 -> 0.15.4 2020-01-23 02:53:09 +00:00
py-xenaPython
pyfasta
python-nexus
rainbow Update WWW 2020-03-31 23:18:09 +00:00
recombine
ruby-bio biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser 2020-05-05 14:22:09 +00:00
rubygem-bio
samtools
seaview biology/seaview: Update version 5.0=>5.0.2 2020-03-22 16:54:04 +00:00
seqan
seqan1 Fix some misspelled or duplicated LICENSE_* 2019-09-17 19:21:45 +00:00
seqan-apps devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
seqio
seqtk
sim4
slclust
smithwaterman
stacks
star biology/star: Upgrade to 2.7.3a 2020-04-09 12:43:03 +00:00
stringtie biology/stringtie: fix build on GCC architectures 2020-02-23 10:52:44 +00:00
tabixpp
tophat Deprecate some ports using deprecated version of python 2020-03-08 17:01:46 +00:00
treekin Fix math/openblas and bump dependent ports 2020-01-30 14:17:44 +00:00
treepuzzle
trimadap
trimmomatic Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
tRNAscan-SE biology/tRNAscan-SE: update to 2.0.5 2020-01-13 17:36:57 +00:00
ugene - Resurrect and unbreak by updating to version 34.0 2020-05-10 15:42:32 +00:00
vcflib
vcftools
velvet
viennarna - update libgd to 2.3.0 2020-05-04 21:31:39 +00:00
vsearch biology/vsearch: Upgrade to 2.14.2 2020-02-19 22:34:36 +00:00
wise a-b: Add missing USES={gnome,php,sdl,xorg} 2019-11-08 09:27:56 +00:00
Makefile - Resurrect and unbreak by updating to version 34.0 2020-05-10 15:42:32 +00:00